The in-form Argentina striker slotted the ball into an empty net from an Alexandre Lacazette cross in the 28th minute to give the seven-times league champions their fifth French Cup victory.
Lyon, who are fourth in Ligue 1 and lost the League Cup final to Olympique Marseille two weeks ago, have now secured a spot in the Europa League playoff round.
They were in total control but wasted numerous clear-cut chances against Quevilly.
The third division side, who ousted Marseille in the quarter-finals and Stade Rennes in the last four, went closest to a goal when Lyon keeper Hugo Lloris diverted a powerful Anthony Laup shot on to the woodwork in the 66th minute.
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